new version causing weird menu activity

I’m not sure where to get support for this plugin…is it still supported?

Our BadgeOS installation is suddenly not mapping menu items to the correct Badge. For example, if I click the menu item, which is mapped to a particular badge, it takes me to the badge page listed above that menu item. Recently updated the site the WordPress 4.6.1 and we are using the Catch Everest theme. All of the plugins are up to date. Any ideas?
I tried different themes, and it happens on some but not others, but definitely happens more than not. However, if I activate the default theme (2016), the weird mapping doesn’t occur. However there are still errors in the log:

They alternate between these 2:
PHP Fatal error: Call to undefined function get_header() in /wp-content/themes/basic/index.php on line 1
Directory index forbidden by Options directive: /wp-includes/css/

From what I’ve read, these errors either indicate an issue with the htaccess file or the index.php, neither of which have changed on our site.